Starting phenix.real_space_refine on Mon Jul 6 10:49:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v82_43015/07_2026/8v82_43015_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v82_43015/07_2026/8v82_43015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v82_43015/07_2026/8v82_43015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v82_43015/07_2026/8v82_43015.map" model { file = "/net/cci-nas-00/data/ceres_data/8v82_43015/07_2026/8v82_43015_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v82_43015/07_2026/8v82_43015_trim.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 115 5.16 5 Cl 10 4.86 5 C 11450 2.51 5 N 2645 2.21 5 O 3200 1.98 5 H 15825 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33265 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6414 Chain: "B" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6414 Chain: "C" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6414 Chain: "D" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6414 Chain: "E" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6414 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 275 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 223 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 223 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 223 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 171 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 2} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 9.97, per 1000 atoms: 0.30 Number of scatterers: 33265 At special positions: 0 Unit cell: (102.505, 101.426, 161.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 5 19.99 Cl 10 17.00 S 115 16.00 P 15 15.00 O 3200 8.00 N 2645 7.00 C 11450 6.00 H 15825 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.05 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.05 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.05 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.05 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 602 " - " ASN A 67 " " NAG B 604 " - " ASN B 67 " " NAG C 604 " - " ASN C 67 " " NAG D 604 " - " ASN D 67 " " NAG E 604 " - " ASN E 67 " " NAG F 1 " - " ASN A 23 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN B 23 " " NAG I 1 " - " ASN B 110 " " NAG J 1 " - " ASN C 23 " " NAG K 1 " - " ASN C 110 " " NAG L 1 " - " ASN D 23 " " NAG M 1 " - " ASN D 110 " " NAG N 1 " - " ASN E 23 " " NAG O 1 " - " ASN E 110 " Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.5 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 44.5% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.724A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 214 through 227 removed outlier: 3.637A pdb=" N LEU A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 237 through 260 removed outlier: 4.569A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 409 through 465 Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.540A pdb=" N PHE A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.723A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.637A pdb=" N LEU B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 237 through 260 removed outlier: 4.568A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 409 through 465 Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.540A pdb=" N PHE B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.724A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.637A pdb=" N LEU C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 237 through 260 removed outlier: 4.569A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 409 through 465 Processing helix chain 'C' and resid 469 through 478 removed outlier: 3.540A pdb=" N PHE C 478 " --> pdb=" O VAL C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.723A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 227 removed outlier: 3.637A pdb=" N LEU D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 237 through 260 removed outlier: 4.569A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 409 through 465 Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.540A pdb=" N PHE D 478 " --> pdb=" O VAL D 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.724A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 227 removed outlier: 3.637A pdb=" N LEU E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 232 through 236 Processing helix chain 'E' and resid 237 through 260 removed outlier: 4.569A pdb=" N VAL E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 409 through 465 Processing helix chain 'E' and resid 469 through 478 removed outlier: 3.540A pdb=" N PHE E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 48 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP C 41 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR C 60 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR C 29 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.543A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.543A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP D 41 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR D 60 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR D 29 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.507A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.507A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL E 48 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP E 41 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR E 60 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR E 29 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) 971 hydrogen bonds defined for protein. 2838 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.82 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 15785 1.05 - 1.25: 2620 1.25 - 1.46: 6618 1.46 - 1.67: 8487 1.67 - 1.87: 180 Bond restraints: 33690 Sorted by residual: bond pdb=" NZ LYS B 75 " pdb=" HZ3 LYS B 75 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" NZ LYS C 181 " pdb=" HZ2 LYS C 181 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS D 124 " pdb=" HZ2 LYS D 124 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS B 303 " pdb=" HZ3 LYS B 303 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS B 191 " pdb=" HZ1 LYS B 191 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 33685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 55600 2.55 - 5.10: 4485 5.10 - 7.64: 140 7.64 - 10.19: 0 10.19 - 12.74: 5 Bond angle restraints: 60230 Sorted by residual: angle pdb=" O11 POV D 605 " pdb=" P POV D 605 " pdb=" O12 POV D 605 " ideal model delta sigma weight residual 97.67 110.41 -12.74 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 POV A 603 " pdb=" P POV A 603 " pdb=" O12 POV A 603 " ideal model delta sigma weight residual 97.67 110.40 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 POV A 608 " pdb=" P POV A 608 " pdb=" O12 POV A 608 " ideal model delta sigma weight residual 97.67 110.39 -12.72 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 POV C 605 " pdb=" P POV C 605 " pdb=" O12 POV C 605 " ideal model delta sigma weight residual 97.67 110.38 -12.71 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 POV B 605 " pdb=" P POV B 605 " pdb=" O12 POV B 605 " ideal model delta sigma weight residual 97.67 110.38 -12.71 3.00e+00 1.11e-01 1.79e+01 ... (remaining 60225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.78: 16267 29.78 - 59.56: 568 59.56 - 89.35: 125 89.35 - 119.13: 35 119.13 - 148.91: 20 Dihedral angle restraints: 17015 sinusoidal: 9840 harmonic: 7175 Sorted by residual: dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N CYS A 190 " pdb=" CA CYS A 190 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N CYS B 190 " pdb=" CA CYS B 190 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 17012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2132 0.063 - 0.125: 481 0.125 - 0.188: 98 0.188 - 0.250: 14 0.250 - 0.313: 15 Chirality restraints: 2740 Sorted by residual: chirality pdb=" C1 EPJ E 607 " pdb=" C2 EPJ E 607 " pdb=" C6 EPJ E 607 " pdb=" C7 EPJ E 607 " both_signs ideal model delta sigma weight residual False -2.85 -2.54 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C1 EPJ B 608 " pdb=" C2 EPJ B 608 " pdb=" C6 EPJ B 608 " pdb=" C7 EPJ B 608 " both_signs ideal model delta sigma weight residual False -2.85 -2.54 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C1 EPJ A 606 " pdb=" C2 EPJ A 606 " pdb=" C6 EPJ A 606 " pdb=" C7 EPJ A 606 " both_signs ideal model delta sigma weight residual False -2.85 -2.54 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 2737 not shown) Planarity restraints: 4740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 604 " -0.285 2.00e-02 2.50e+03 2.45e-01 7.52e+02 pdb=" C7 NAG E 604 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG E 604 " 0.002 2.00e-02 2.50e+03 pdb=" N2 NAG E 604 " 0.418 2.00e-02 2.50e+03 pdb=" O7 NAG E 604 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " -0.284 2.00e-02 2.50e+03 2.45e-01 7.52e+02 pdb=" C7 NAG A 602 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.002 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " 0.418 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 604 " 0.284 2.00e-02 2.50e+03 2.45e-01 7.52e+02 pdb=" C7 NAG D 604 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG D 604 " -0.002 2.00e-02 2.50e+03 pdb=" N2 NAG D 604 " -0.418 2.00e-02 2.50e+03 pdb=" O7 NAG D 604 " 0.202 2.00e-02 2.50e+03 ... (remaining 4737 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 2776 2.25 - 2.84: 72383 2.84 - 3.43: 85644 3.43 - 4.01: 125031 4.01 - 4.60: 188563 Nonbonded interactions: 474397 Sorted by model distance: nonbonded pdb=" OE2 GLU B 18 " pdb=" HH TYR B 63 " model vdw 1.667 2.450 nonbonded pdb=" OE2 GLU E 18 " pdb=" HH TYR E 63 " model vdw 1.667 2.450 nonbonded pdb=" OE2 GLU C 18 " pdb=" HH TYR C 63 " model vdw 1.668 2.450 nonbonded pdb=" OE2 GLU A 18 " pdb=" HH TYR A 63 " model vdw 1.668 2.450 nonbonded pdb=" OE2 GLU D 18 " pdb=" HH TYR D 63 " model vdw 1.669 2.450 ... (remaining 474392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 478)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 36.340 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 17905 Z= 0.363 Angle : 1.050 12.742 24375 Z= 0.510 Chirality : 0.060 0.313 2740 Planarity : 0.012 0.245 2870 Dihedral : 19.392 148.910 7650 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.17), residues: 1955 helix: -0.50 (0.16), residues: 790 sheet: -1.05 (0.21), residues: 460 loop : -1.23 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 309 TYR 0.017 0.003 TYR B 273 PHE 0.012 0.002 PHE E 99 TRP 0.019 0.002 TRP D 307 HIS 0.004 0.001 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.36 (17865) covalent geometry : angle 1.03056 / 0.51 (24265) SS BOND : bond 0.01412 / 0.76 ( 10) SS BOND : angle 3.45459 / 2.16 ( 20) hydrogen bonds : bond 0.15759 / 10.46 ( 866) hydrogen bonds : angle 7.50685 / 5.22 ( 2838) link_BETA1-4 : bond 0.00362 / 0.21 ( 15) link_BETA1-4 : angle 2.09219 / 1.34 ( 45) link_NAG-ASN : bond 0.00483 / 0.29 ( 15) link_NAG-ASN : angle 3.85651 / 2.48 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 156 ASP cc_start: 0.7857 (t0) cc_final: 0.7592 (t0) REVERT: C 278 MET cc_start: 0.7930 (mtp) cc_final: 0.7680 (mtp) REVERT: D 57 MET cc_start: 0.8385 (mtm) cc_final: 0.7946 (mtm) REVERT: E 156 ASP cc_start: 0.7778 (t0) cc_final: 0.7458 (t0) REVERT: E 253 MET cc_start: 0.7881 (mmt) cc_final: 0.7653 (mtp) REVERT: E 278 MET cc_start: 0.7888 (mtp) cc_final: 0.7593 (mtp) REVERT: E 309 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6858 (ttt180) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 1.4025 time to fit residues: 359.4216 Evaluate side-chains 186 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.125595 restraints weight = 67538.432| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.46 r_work: 0.3316 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17905 Z= 0.143 Angle : 0.633 6.351 24375 Z= 0.310 Chirality : 0.041 0.150 2740 Planarity : 0.005 0.035 2870 Dihedral : 18.964 139.732 3885 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.34 % Allowed : 6.72 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 1955 helix: 0.26 (0.16), residues: 805 sheet: -1.03 (0.21), residues: 465 loop : -0.95 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 309 TYR 0.018 0.001 TYR A 187 PHE 0.015 0.001 PHE C 274 TRP 0.012 0.001 TRP B 307 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (17865) covalent geometry : angle 0.61671 / 0.31 (24265) SS BOND : bond 0.00841 / 0.45 ( 10) SS BOND : angle 1.66065 / 0.99 ( 20) hydrogen bonds : bond 0.04563 / 2.98 ( 866) hydrogen bonds : angle 5.47936 / 3.79 ( 2838) link_BETA1-4 : bond 0.00570 / 0.33 ( 15) link_BETA1-4 : angle 1.97026 / 1.40 ( 45) link_NAG-ASN : bond 0.00198 / 0.13 ( 15) link_NAG-ASN : angle 2.55220 / 1.65 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 189 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: B 40 MET cc_start: 0.8581 (mtp) cc_final: 0.8293 (mtp) REVERT: D 40 MET cc_start: 0.8438 (mtp) cc_final: 0.8191 (mtp) REVERT: D 57 MET cc_start: 0.8571 (mtt) cc_final: 0.8220 (mtm) REVERT: E 278 MET cc_start: 0.8252 (mtp) cc_final: 0.7957 (mtp) REVERT: E 303 LYS cc_start: 0.7743 (mmmt) cc_final: 0.7391 (tptp) outliers start: 6 outliers final: 1 residues processed: 191 average time/residue: 1.5050 time to fit residues: 319.4343 Evaluate side-chains 175 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 169 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.148709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124391 restraints weight = 59773.764| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.42 r_work: 0.3286 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17905 Z= 0.184 Angle : 0.611 5.905 24375 Z= 0.306 Chirality : 0.041 0.146 2740 Planarity : 0.005 0.035 2870 Dihedral : 16.573 124.464 3885 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.06 % Allowed : 8.29 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 1955 helix: 0.60 (0.17), residues: 805 sheet: -0.73 (0.21), residues: 465 loop : -0.77 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.016 0.002 TYR B 187 PHE 0.014 0.002 PHE E 99 TRP 0.012 0.002 TRP C 307 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (17865) covalent geometry : angle 0.59354 / 0.30 (24265) SS BOND : bond 0.00878 / 0.48 ( 10) SS BOND : angle 1.63902 / 0.96 ( 20) hydrogen bonds : bond 0.04668 / 3.06 ( 866) hydrogen bonds : angle 5.27943 / 3.65 ( 2838) link_BETA1-4 : bond 0.00415 / 0.22 ( 15) link_BETA1-4 : angle 1.83613 / 1.30 ( 45) link_NAG-ASN : bond 0.00449 / 0.31 ( 15) link_NAG-ASN : angle 2.76005 / 1.79 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: B 174 ASP cc_start: 0.7856 (m-30) cc_final: 0.7545 (m-30) REVERT: C 450 MET cc_start: 0.7987 (ttt) cc_final: 0.7678 (ttp) REVERT: C 466 SER cc_start: 0.8770 (p) cc_final: 0.8501 (p) REVERT: D 429 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7284 (mt-10) REVERT: E 278 MET cc_start: 0.8281 (mtp) cc_final: 0.7997 (mtp) outliers start: 1 outliers final: 1 residues processed: 188 average time/residue: 1.5347 time to fit residues: 320.2610 Evaluate side-chains 176 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 157 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 143 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125152 restraints weight = 60224.156| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.39 r_work: 0.3298 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17905 Z= 0.178 Angle : 0.577 5.633 24375 Z= 0.293 Chirality : 0.040 0.146 2740 Planarity : 0.005 0.035 2870 Dihedral : 15.642 111.333 3885 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.39 % Allowed : 8.29 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.18), residues: 1955 helix: 0.74 (0.17), residues: 810 sheet: -0.62 (0.22), residues: 465 loop : -0.71 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.012 0.002 TYR B 187 PHE 0.012 0.001 PHE D 99 TRP 0.011 0.002 TRP E 307 HIS 0.004 0.001 HIS D 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (17865) covalent geometry : angle 0.56068 / 0.29 (24265) SS BOND : bond 0.00860 / 0.46 ( 10) SS BOND : angle 1.58158 / 0.93 ( 20) hydrogen bonds : bond 0.04364 / 2.86 ( 866) hydrogen bonds : angle 5.15173 / 3.56 ( 2838) link_BETA1-4 : bond 0.00363 / 0.19 ( 15) link_BETA1-4 : angle 1.60284 / 1.13 ( 45) link_NAG-ASN : bond 0.00146 / 0.09 ( 15) link_NAG-ASN : angle 2.63604 / 1.68 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 ASP cc_start: 0.7854 (m-30) cc_final: 0.7541 (m-30) REVERT: B 445 ASP cc_start: 0.6560 (OUTLIER) cc_final: 0.6347 (m-30) REVERT: C 450 MET cc_start: 0.7987 (ttt) cc_final: 0.7682 (ttp) REVERT: D 429 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7338 (mt-10) REVERT: E 278 MET cc_start: 0.8268 (mtp) cc_final: 0.8049 (mtp) REVERT: E 445 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.6490 (m-30) outliers start: 7 outliers final: 4 residues processed: 181 average time/residue: 1.6342 time to fit residues: 325.9944 Evaluate side-chains 183 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 102 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 164 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126921 restraints weight = 62579.740| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.41 r_work: 0.3337 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17905 Z= 0.126 Angle : 0.533 5.318 24375 Z= 0.268 Chirality : 0.039 0.142 2740 Planarity : 0.004 0.038 2870 Dihedral : 15.015 102.254 3885 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.22 % Allowed : 8.52 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.18), residues: 1955 helix: 1.10 (0.17), residues: 795 sheet: -0.57 (0.22), residues: 475 loop : -0.58 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 446 TYR 0.008 0.001 TYR D 273 PHE 0.013 0.001 PHE C 274 TRP 0.009 0.001 TRP E 307 HIS 0.002 0.000 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (17865) covalent geometry : angle 0.51807 / 0.26 (24265) SS BOND : bond 0.00823 / 0.44 ( 10) SS BOND : angle 1.36889 / 0.80 ( 20) hydrogen bonds : bond 0.04037 / 2.64 ( 866) hydrogen bonds : angle 4.91627 / 3.39 ( 2838) link_BETA1-4 : bond 0.00361 / 0.20 ( 15) link_BETA1-4 : angle 1.37550 / 0.96 ( 45) link_NAG-ASN : bond 0.00065 / 0.03 ( 15) link_NAG-ASN : angle 2.50943 / 1.61 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 183 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 ASP cc_start: 0.7712 (m-30) cc_final: 0.7406 (m-30) REVERT: C 450 MET cc_start: 0.7985 (ttt) cc_final: 0.7692 (ttp) REVERT: D 57 MET cc_start: 0.8524 (mtt) cc_final: 0.8289 (mtm) REVERT: D 429 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7307 (mt-10) REVERT: E 185 ARG cc_start: 0.6591 (ttt180) cc_final: 0.6375 (ttt180) REVERT: E 278 MET cc_start: 0.8255 (mtp) cc_final: 0.8007 (mtp) outliers start: 4 outliers final: 4 residues processed: 184 average time/residue: 1.6308 time to fit residues: 333.1294 Evaluate side-chains 176 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 15 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.147539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123108 restraints weight = 65991.368| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.47 r_work: 0.3279 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17905 Z= 0.241 Angle : 0.620 6.310 24375 Z= 0.318 Chirality : 0.042 0.150 2740 Planarity : 0.005 0.049 2870 Dihedral : 15.221 100.953 3885 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.45 % Allowed : 8.46 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.18), residues: 1955 helix: 0.97 (0.17), residues: 795 sheet: -0.46 (0.22), residues: 460 loop : -0.74 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 4 TYR 0.015 0.002 TYR D 128 PHE 0.019 0.002 PHE E 99 TRP 0.012 0.002 TRP D 307 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (17865) covalent geometry : angle 0.60507 / 0.31 (24265) SS BOND : bond 0.00838 / 0.45 ( 10) SS BOND : angle 1.69731 / 0.99 ( 20) hydrogen bonds : bond 0.04690 / 3.08 ( 866) hydrogen bonds : angle 5.23178 / 3.61 ( 2838) link_BETA1-4 : bond 0.00233 / 0.12 ( 15) link_BETA1-4 : angle 1.45607 / 1.01 ( 45) link_NAG-ASN : bond 0.00217 / 0.13 ( 15) link_NAG-ASN : angle 2.74405 / 1.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: B 445 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6387 (m-30) REVERT: C 450 MET cc_start: 0.8012 (ttt) cc_final: 0.7705 (ttp) REVERT: D 234 ASP cc_start: 0.7712 (m-30) cc_final: 0.7463 (m-30) REVERT: D 429 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7382 (mt-10) REVERT: E 278 MET cc_start: 0.8298 (mtp) cc_final: 0.8097 (mtp) outliers start: 8 outliers final: 4 residues processed: 174 average time/residue: 1.5979 time to fit residues: 308.0703 Evaluate side-chains 177 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 172 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 10 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 172 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126085 restraints weight = 61465.744| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.41 r_work: 0.3326 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17905 Z= 0.136 Angle : 0.543 5.749 24375 Z= 0.275 Chirality : 0.039 0.145 2740 Planarity : 0.004 0.035 2870 Dihedral : 14.611 92.031 3885 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.28 % Allowed : 8.96 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 1955 helix: 1.14 (0.17), residues: 795 sheet: -0.46 (0.22), residues: 460 loop : -0.58 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.010 0.001 TYR A 273 PHE 0.009 0.001 PHE B 99 TRP 0.010 0.001 TRP D 307 HIS 0.003 0.001 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (17865) covalent geometry : angle 0.52908 / 0.27 (24265) SS BOND : bond 0.00814 / 0.44 ( 10) SS BOND : angle 1.44783 / 0.85 ( 20) hydrogen bonds : bond 0.04089 / 2.67 ( 866) hydrogen bonds : angle 4.94384 / 3.41 ( 2838) link_BETA1-4 : bond 0.00319 / 0.17 ( 15) link_BETA1-4 : angle 1.32889 / 0.92 ( 45) link_NAG-ASN : bond 0.00071 / 0.05 ( 15) link_NAG-ASN : angle 2.47403 / 1.59 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8348 (ttmm) cc_final: 0.8135 (mtpt) REVERT: B 174 ASP cc_start: 0.7851 (m-30) cc_final: 0.7639 (m-30) REVERT: D 234 ASP cc_start: 0.7687 (m-30) cc_final: 0.7435 (m-30) REVERT: D 309 ARG cc_start: 0.7053 (ttm-80) cc_final: 0.6670 (ttt180) REVERT: D 436 GLU cc_start: 0.7739 (tt0) cc_final: 0.7520 (tt0) REVERT: E 278 MET cc_start: 0.8274 (mtp) cc_final: 0.8055 (mtp) outliers start: 5 outliers final: 4 residues processed: 178 average time/residue: 1.4173 time to fit residues: 279.8887 Evaluate side-chains 180 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 105 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125914 restraints weight = 62236.204| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.43 r_work: 0.3309 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17905 Z= 0.148 Angle : 0.543 6.372 24375 Z= 0.275 Chirality : 0.039 0.144 2740 Planarity : 0.004 0.036 2870 Dihedral : 14.239 84.262 3885 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.45 % Allowed : 8.85 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 1955 helix: 1.20 (0.17), residues: 795 sheet: -0.39 (0.23), residues: 460 loop : -0.53 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.010 0.001 TYR A 273 PHE 0.012 0.001 PHE C 274 TRP 0.011 0.001 TRP D 307 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (17865) covalent geometry : angle 0.52937 / 0.27 (24265) SS BOND : bond 0.00824 / 0.44 ( 10) SS BOND : angle 1.50355 / 0.89 ( 20) hydrogen bonds : bond 0.04105 / 2.68 ( 866) hydrogen bonds : angle 4.89648 / 3.37 ( 2838) link_BETA1-4 : bond 0.00297 / 0.16 ( 15) link_BETA1-4 : angle 1.30430 / 0.90 ( 45) link_NAG-ASN : bond 0.00076 / 0.05 ( 15) link_NAG-ASN : angle 2.44438 / 1.58 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8119 (mtpt) REVERT: B 445 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.6231 (m-30) REVERT: D 234 ASP cc_start: 0.7698 (m-30) cc_final: 0.7442 (m-30) REVERT: D 429 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7327 (mt-10) REVERT: E 278 MET cc_start: 0.8289 (mtp) cc_final: 0.8061 (mtp) outliers start: 8 outliers final: 5 residues processed: 182 average time/residue: 1.4830 time to fit residues: 298.9328 Evaluate side-chains 181 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 93 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 0.0770 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123624 restraints weight = 64897.943| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.45 r_work: 0.3289 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17905 Z= 0.225 Angle : 0.605 6.828 24375 Z= 0.309 Chirality : 0.041 0.150 2740 Planarity : 0.005 0.047 2870 Dihedral : 14.305 86.156 3885 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.45 % Allowed : 8.91 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.18), residues: 1955 helix: 1.08 (0.17), residues: 795 sheet: -0.37 (0.22), residues: 460 loop : -0.63 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 309 TYR 0.013 0.002 TYR D 128 PHE 0.018 0.002 PHE C 274 TRP 0.013 0.002 TRP D 307 HIS 0.005 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (17865) covalent geometry : angle 0.59036 / 0.31 (24265) SS BOND : bond 0.00834 / 0.45 ( 10) SS BOND : angle 1.68488 / 0.99 ( 20) hydrogen bonds : bond 0.04535 / 2.97 ( 866) hydrogen bonds : angle 5.13536 / 3.54 ( 2838) link_BETA1-4 : bond 0.00240 / 0.12 ( 15) link_BETA1-4 : angle 1.38548 / 0.95 ( 45) link_NAG-ASN : bond 0.00176 / 0.11 ( 15) link_NAG-ASN : angle 2.64270 / 1.72 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 0.944 Fit side-chains REVERT: A 12 LYS cc_start: 0.8400 (ttmm) cc_final: 0.8150 (mtpt) REVERT: B 445 ASP cc_start: 0.6566 (OUTLIER) cc_final: 0.6271 (m-30) REVERT: D 234 ASP cc_start: 0.7710 (m-30) cc_final: 0.7440 (m-30) REVERT: E 278 MET cc_start: 0.8326 (mtp) cc_final: 0.8102 (mtp) outliers start: 8 outliers final: 4 residues processed: 175 average time/residue: 1.5285 time to fit residues: 298.2285 Evaluate side-chains 172 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 167 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 115 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 173 optimal weight: 0.0370 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127021 restraints weight = 62708.515| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.43 r_work: 0.3339 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17905 Z= 0.116 Angle : 0.525 6.363 24375 Z= 0.266 Chirality : 0.038 0.149 2740 Planarity : 0.004 0.050 2870 Dihedral : 13.516 79.744 3885 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.28 % Allowed : 9.24 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 1955 helix: 1.25 (0.17), residues: 795 sheet: -0.48 (0.23), residues: 465 loop : -0.44 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 309 TYR 0.011 0.001 TYR A 273 PHE 0.016 0.001 PHE C 274 TRP 0.011 0.001 TRP D 307 HIS 0.002 0.000 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (17865) covalent geometry : angle 0.51252 / 0.26 (24265) SS BOND : bond 0.00830 / 0.44 ( 10) SS BOND : angle 1.36885 / 0.81 ( 20) hydrogen bonds : bond 0.03911 / 2.55 ( 866) hydrogen bonds : angle 4.81286 / 3.32 ( 2838) link_BETA1-4 : bond 0.00311 / 0.17 ( 15) link_BETA1-4 : angle 1.27232 / 0.87 ( 45) link_NAG-ASN : bond 0.00118 / 0.07 ( 15) link_NAG-ASN : angle 2.33419 / 1.51 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 181 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8369 (ttmm) cc_final: 0.8124 (mtpt) REVERT: B 174 ASP cc_start: 0.7693 (m-30) cc_final: 0.7471 (m-30) REVERT: B 445 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6456 (m-30) REVERT: C 274 PHE cc_start: 0.8432 (m-10) cc_final: 0.8216 (m-10) REVERT: D 234 ASP cc_start: 0.7684 (m-30) cc_final: 0.7425 (m-30) REVERT: D 429 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7326 (mt-10) REVERT: E 278 MET cc_start: 0.8284 (mtp) cc_final: 0.8042 (mtp) outliers start: 5 outliers final: 5 residues processed: 183 average time/residue: 1.4523 time to fit residues: 296.3081 Evaluate side-chains 188 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.149170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124916 restraints weight = 67564.463| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.47 r_work: 0.3293 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17905 Z= 0.167 Angle : 0.555 6.413 24375 Z= 0.283 Chirality : 0.039 0.145 2740 Planarity : 0.005 0.046 2870 Dihedral : 13.397 81.730 3885 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.39 % Allowed : 9.36 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 1955 helix: 1.25 (0.17), residues: 795 sheet: -0.35 (0.23), residues: 460 loop : -0.51 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 309 TYR 0.011 0.002 TYR E 187 PHE 0.017 0.001 PHE C 274 TRP 0.012 0.001 TRP D 307 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (17865) covalent geometry : angle 0.54172 / 0.28 (24265) SS BOND : bond 0.00828 / 0.45 ( 10) SS BOND : angle 1.54421 / 0.91 ( 20) hydrogen bonds : bond 0.04169 / 2.73 ( 866) hydrogen bonds : angle 4.92219 / 3.40 ( 2838) link_BETA1-4 : bond 0.00279 / 0.15 ( 15) link_BETA1-4 : angle 1.29873 / 0.89 ( 45) link_NAG-ASN : bond 0.00090 / 0.06 ( 15) link_NAG-ASN : angle 2.41975 / 1.57 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11674.31 seconds wall clock time: 198 minutes 11.24 seconds (11891.24 seconds total)